Emory R Workshop: November 11, 2022

Rollins COVID-19 Epidemiology Fellowship R Training

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Workshop Instructor:

• Melinda Higgins, PhD
  • Director Biostatistics and Data Core
  • Office of Nursing Research
  • School of Nursing - Emory University
  • melinda.higgins@emory.edu

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Table of Contents

• Preparation for Workshop
• R packages to be installed for workshop:
• Overview of Workshop
• Schedule - links to slides and R scripts
• Workshop Recording
• Learn more about Rmarkdown at:
• More R Resources - get help and inspiration

Preparation for Workshop

1. Install R https://cran.r-project.org/
   • see instructions on installing R in chapter 1 of Modern Dive Book
2. Install RStudio Desktop https://posit.co/download/rstudio-desktop/
   • • see instructions on installing R in chapter 1 of Modern Dive Book
3. Install the R packages listed below.
   • see instruction on how to install packages at Chapter 1.3.1 in the Modern Dive Book.
4. Download datasets and mapfiles:
   • abalone.csv - CSV format
   • abalone.RData - R Binary format
   • abalone.sas7bdat - SAS format
   • abalone.sav - SPSS format
   • abalone.xlsx - EXCEL XLSX format
   • abalone dataset at UCI library
   • Fulton County Map Shapefiles - ZIP file
   • FALSE GA COVID DATA - EXCEL file

OPTIONAL PREP

1. OPTIONAL if you are still actively enrolled in RSPH, you can also run R and RStudio in the Emory RSPH virtual desktop using Apporto, https://rsphemory.apporto.com/.
2. Online BOOKS to get started:
   1. Statistical Inference via Data Science: A ModernDive into R and the Tidyverse! by Chester Ismay and Albert Y. Kim https://moderndive.netlify.app/.
   2. R in Action, Third Edition: Data analysis and graphics with R and Tidyverse by Robert I. Kabacoff https://www.manning.com/books/r-in-action-third-edition
   3. The Epidemiologist R Handbook https://epirhandbook.com/en/

R packages to be installed for workshop:

See packages listed on CRAN - click on “Packages”. All of the packages on CRAN can be installed inside RStudio by clicking on “Tools/Install Packages” top menu.

• tidyverse website on tidyverse on CRAN- which includes:
  • ggplot2 website and on CRAN
  • dplyr website
  • readr website and on CRAN
  • haven website and on CRAN and more packages are included
• palmerpenguins website and on CRAN
• patchwork website and on CRAN
• Hmisc website and on CRAN
• psych website and on CRAN
• arsenal website and on CRAN
• readxl website and on CRAN
• foreign on CRAN
• ggthemes on CRAN
• data.table website and on CRAN
• sf website and on CRAN

• leaflet website and on CRAN

• OPTIONAL ggthemr on Github - this one is not yet on CRAN and is totally optional to install. For this you will need the devtools package which is available on CRAN. Once you have devtools installed, you can optionally install the ggthemr package by typing the following command:

devtools::install_github('Mikata-Project/ggthemr')

Overview of Workshop

This workshop will cover (final list in development):

• Module 01
  • An introduction to R and RStudio
  • Learning about R Objects and data structures
• Module 02
  • Introduction to R packages
  • Loading data, Saving data (read/write datasets)
• Module 03
  • Data Visualization with ggplot2 package
• Module 04
  • Brief Intro Data Wrangling with dplyr package
• Module 05
  • Introduction to Rmarkdown
  • Exercise - creating Rmarkdown Report
• Module 06
  • Using dplyr to join datasets
• Module 07
  • Putting it all together into a “COVID Case Report”
• Module 08
  • Open Dialog - audience questions

Schedule - links to slides and R scripts

November 11, 2022
09:00 - 16:00

Time	Activity
09:00 - 09:25	Module 1 [Slides and R script]
09:25 - 09:50	Module 2 [Slides and R script]
09:50 - 10:00	BIO Break
10:00 - 10:30	Module 3 [Slides and R script]
	R Scripts w/Answers
10:30 - 11:00	Module 4 [Slides and R script]
	R Scripts w/Answers
11:00 - 12:00	Breakout Session 1 [working on exercises from above modules]
12:00 - 13:00	LUNCH BREAK
13:00 - 13:25	Module 5 Abalone Rmarkdown Report and Rmarkdown file
	Abalone RMarkdown w/Answers Rmarkdown file
13:25 - 13:50	Module 6 Merging Datasets Exercise and Rmarkdown file
	data1.csv
	data2.csv
	data.table exercise R script
13:50 - 14:00	BIO Break
14:00 - 14:30	Module 7 COVID Cases Report and Rmarkdown file
14:30 - 15:00	Module 8 Open Q&A
15:00 - 16:00	Breakout Session 2 [working on exercises from modules and more editing on COVID case report]

Workshop Recording

• To be added later…

Learn more about Rmarkdown at:

• Rmarkdown by RStudio
• R Markdown: The Definitive Guide
• R Markdown Cookbook
• Example Blog http://jenrichmond.rbind.io/post/2021-08-31-parameterised-penguins/
• Example Document https://rpubs.com/jenrichmond/adelie

More R Resources - get help and inspiration

• RStudio Education
• Quick-R
• BOOK: R in Action, 3rd ed.
• Datacamp
  • R for SAS Users - My Datacamp Course
• Coursera
  • Reproducible Templates for Analysis and Dissemination - My Coursera Course
• My Emory Courses:
  • Emory N741
  • Emory N736
• BOOK: Statistical Inference via Data Science
• BOOK: The Epidemiologist R Handbook
• BOOK: R Graphics Cookbook, 2nd edition by Winston Chang and associated R Graphics Cookbook website
• The R Graph Gallery